How to render multiple (say 1000) overlapping objects seperately (one per frame)?
Based on a previous answer I would use a script that imports each stl file and keyframes the visibility as it goes.

import bpy
scn = bpy.context.scene
for f in range(scn.frame_start, scn.frame_end):
    fpath = bpy.path.abspath('//sim_data_{}.stl'.format(f))
    bpy.ops.import_mesh.stl(filepath=fpath)
    obj = bpy.context.active_object
    # key as visible on the current frame
    obj.keyframe_insert('hide',frame=f)
    obj.keyframe_insert('hide_render',frame=f)
    # hide it
    obj.hide = True
    obj.hide_render = True
    # key as hidden on the previous frame
    obj.keyframe_insert('hide',frame=f-1)
    obj.keyframe_insert('hide_render',frame=f-1)
    # key as hidden on the next frame
    obj.keyframe_insert('hide',frame=f+1)
    obj.keyframe_insert('hide_render',frame=f+1)